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Satchu's Rich Wrap-Up
 
 
Monday 13th of September 2021
 
Morning
Africa


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Cruz-Diez Induction Chromatique 88 Museum of Fine Arts, Houston, USA
Misc.


Carlos Cruz-Diez A major protagonist in the field of Kinetic and Optical Art, a movement that encourages “an awareness of the instability of reality''

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Welcome to Benguela @mailandguardian @thecontinent_ @CaipLounge
Africa



Benguela exists within Angola’s collective psyche in a way no other city does. 

It’s a place that’s inspired poets, musicians, writers and artists, a frequent subject of their adoration and longing.

The second-oldest Portuguese-founded city in Angola, Benguela has existed since May 17 1617 and is located in the western part of the country. 

As a coastal city – a cidade das acácias rubras (city of the Royal Poinciana tree), as Benguela is known – it is spoilt for beaches, fresh seafood, the type of climate that makes you want to constantly be outside, and gorgeous people with open hearts.
It wasn’t always like this, of course.
Perhaps the darkest part of this city’s history coincides with its colonial past, when Benguela was a major slave port. 

No other country in Africa exported more slaves to South America, specifically Brazil, than Angola, and a countless number of them left from these very shores.
From Benguela’s fabled Praia Morena, where slaves were loaded, it’s a straight shot to Salvador da Bahia on the other side of the Atlantic.
Paradoxically, as it constantly is with history, Benguela’s colonial past richly contributes to the architecture that gives this city its charm. 

The wide, tree-lined avenues are dotted with centuries-old churches and palaces, gardens and plazas, and on the edges of the city are sprawling shanty towns to remind us of all the refugees that arrived from the interior, driven by Angola’s decades-long civil war .
A city of more than 600,000 people, Benguela is surprisingly small, compact and easy to navigate. 

The best way to get around is by kupapata, the ubiquitous motorcycles that carry everyone around (trips start at 150AKZ – about 25 US cents), but sometimes, especially in the historic centre, it’s just better to go on foot. 

There are actual sidewalks, something those from the capital city Luanda have forgotten exists, and the varied architecture of houses, cinemas (the open-aired Cine Kalunga (1) and the majestic Teatro Monumental are a must) and government offices are visually arresting.
To further delve into Benguela’s past, the Archeology Museum, one of the oldest buildings still standing in the city, is a must.  

The museum no longer houses much, but in centuries past slaves were held here before being put on wooden vessels that sailed to Brazil and Cuba.

To clear your head, exit the museum and take a stroll down Praia Morena (2), Benguela’s very own urban beach (the water has seen cleaner days, though), and enjoy the casuarinas and the people-watching, then down a Cuca beer or two at nearby O Boteco.
A deeply Catholic city, Benguela has several significant churches. Among the more famous ones are the Our Lady of Fátima Cathedral (3), an imposing triangular structure that took 40 years to complete, and the unmistakable Our Lady of Pópulo, an architectural treasure built in the 17th century with stones brought over from Brazil to steady the slave ships as they made their journey back. 

Close by, the Palácio das Bolas (4), a palace built in 1920, is one of Benguela’s most recognisable landmarks; today, it serves as the ruling party’s provincial headquarters.
Of course, you can’t visit Benguela without taking a swim in one of its beautiful beaches. 

The best one closest to the city is Baía Azul, a short, breezy 25 minute drive along the coast. 

Baía Azul is where Benguela goes to unwind, and many locals and out-of-towners built vacation homes on the hills overlooking the serene blue waters. 

For 5,000AKZ ($8), have yourself some freshly caught grilled fish or lobster with a side of feijão de óleo de palma (beans stewed in palm oil) and a beer on the picnic tables at Restaurante Bodona, with your feet firmly planted on the sand as your eyes scan the Atlantic’s horizon.
Bodona is good and the setting is hard to beat, but perhaps the best place to eat in town is at Tudo na Brasa. 

Their specialty: traditional Portuguese roasted suckling pig, in which the pork meat is juicy and tender while the skin is satisfyingly crisp. 

It’s served alongside a distinctive sauce made of lard, a splash of white wine, garlic and lots of white pepper. (It’ll set you back about $10.) 

Such is Portuguese influence in coastal Angola and especially Benguela that one of its favourite dishes is a perfected version of this Iberian favourite.
The band África Tentação sang warmly about the city in their iconic 1982 jam Quando Fui à Benguela (When I Went to Benguela). 

Even though the song is in Portuguese, you’ll be able to make out some of the landmarks mentioned here.
“When I went to Benguela I didn’t want to leave,” they sing. “When I saw Praia Morena I started dreaming.” 

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She Says we are not Afraid of Death, We the New Generation will fight for Our Freedom and Rights. @IhteshamAfghan
Law & Politics



A Brave Afghan Woman in front of Talibans In Kabul Demanding Freedom of Speech, Democracy and Right ro Resist Invasion. She Says we are not Afraid of Death, We the New Generation will fight for Our Freedom and Rights.

An Afghan woman fearlessly stands face to face with a Taliban armed man who pointed his gun to her chest. Photo:  @Reuters @ZahraSRahimi


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If there’s one thing we know about climate breakdown, it’s that it will not be linear, smooth or gradual. @guardian
Food, Climate & Agriculture





Current plans to avoid catastrophe would work in a simple system like a washbasin, in which you can close the tap until the inflow is less than the outflow. 

But they are less likely to work in complex systems, such as the atmosphere, oceans and biosphere. 

Complex systems seek equilibrium. When they are pushed too far out of one equilibrium state, they can flip suddenly into another. 

A common property of complex systems is that it’s much easier to push them past a tipping point than to push them back. 

Once a transition has happened, it cannot realistically be reversed.

A common sign that complex systems are approaching tipping points is rising volatility: they start to flicker. 

The extreme weather in 2021 – the heat domes, droughts, fires, floods and cyclones – is, frankly, terrifying. 

If Earth systems tip as a result of global heating, there will be little difference between taking inadequate action and taking no action at all. A miss is as good as a mile.

If Earth systems cross critical thresholds, everything we did and everything we were – the learning, the wisdom, the stories, the art, the politics, the love, the hate, the anger and the hope – will be reduced to stratigraphy. It’s not a smooth and linear transition we need. It’s a crash course.


In chaos theory, the butterfly effect is the sensitive dependence on initial conditions in which a small change in one state of a deterministic nonlinear system can result in large differences in a later state.




23-NOV 2015 I cannot help feeling we are like frogs in boiling water. We have created massive interference in the "cosmic tuning" phenomenon
http://bit.ly/2Nuxi76


In this book, Martin Rees puts forward six equations which govern our universe, a universe so big that we are like a grain of sand on a beach. The mathematics of these equations is so miraculous that Rees speaks to a “cosmic tuning” phenomenon.
For example; Ω ≈ 0.3: the ratio of the actual density of the universe to the critical (minimum) density required for the universe to even- tually collapse under its gravity. Ω determines the ultimate fate of the universe. 

If Ω is greater than one, the universe will experience a big crunch. If Ω is less than one, the universe will expand forever.



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Nations w/ fast COVID19 avg 2wk case/day reduction @jmlukens
Misc.





Indonesia: -53%
Kosovo: -51%
Spain: -51%
Bangladesh: -50%
Argentina: -48%
Georgia: -48%
Japan: -46%
Morocco: -45%
South Africa: -43%
France: -42%



23-AUG-2021 :: But Holmes was startled. “This virus has gone up three notches in effectively a year and that, I think, was the biggest surprise to me” 





But Holmes was startled. “This virus has gone up three notches in effectively a year and that, I think, was the biggest surprise to me”
The 1918–19 influenza pandemic also appears to have caused more serious illness as time went on, says Lone Simonsen, an epidemiologist at Roskilde University who studies past pandemics.

 “Our data from Denmark suggests it was six times deadlier in the second wave.”

“Many still see Alpha and Delta as being as bad as things are ever going to get,” he says. 

“It would be wise to consider them as steps on a possible trajectory that may challenge our public health response further.”
Some dangerous variants may only be possible if the virus hits on a very rare, winning combination of mutations, Eugene Koonin told me. 

“But with all these millions of infected people, it may very well find that combination.” @kakape 




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Delta took over almost the whole world now @TWenseleers
Misc.




"The greatest shortcoming of the human race is our inability to understand the exponential function." - Professor Allen Bartlett



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As to the goal of reaching herd immunity— “With the emergence of Delta, I realized that it’s just impossible to reach that,” says Müge Çevik University of St. Andrews. Via @ScienceMagazine @kakape
Misc.




The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines


We have now crossed peak Vaccine Euphoria



"Over 50,000 people have died with #COVID19 every week since October last year and for the past month, deaths have remained at almost 70,000 a week”, says @DrTedros @kakape


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―They fancied themselves free, wrote Camus, ―and no one will ever be free so long as there are pestilences
Misc.


―In this respect, our townsfolk were like everybody else, wrapped up in themselves; in other words, they were humanists: they disbelieved in pestilences.
A pestilence isn't a thing made to man's measure; therefore we tell ourselves that pestilence is a mere bogy of the mind, a bad dream that will pass away.
But it doesn't always pass away and, from one bad dream to another, it is men who pass away, and the humanists first of all, because they have taken no precautions

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Currency Markets at a Glance WSJ
World Currencies


Euro 1.1790
Dollar Index 92.764
Japan Yen 110.00
Swiss Franc 0.9194
Pound 1.3818
Aussie 0.7339
India Rupee 73.73
South Korea Won 1176.395
Brazil Real 5.2488
Egypt Pound 15.7459
South Africa Rand 14.2526

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WHO regional overviews – Epidemiological week 30 Aug–5 Sep 2021 African Region
Africa




The African Region continued to report substantial declines in incidence of both cases and deaths. 

This week the Region reported over 110 000 new cases and over 2800 new deaths, decreases of 25% and 26%, respectively, as compared to the previous week. 

These declining trends for the Region’s third wave are encouraging, and largely driven by continued declines in South Africa. 

Nonetheless, several countries continued to report increasing trends in cases (> 30%) this week while mortality continued to increase, albeit at a lower proportion (>10%) in five countries. 


"The #COVID19 third wave in #Africa has taken a downwards slide, with a 23% decrease in new cases last week, driven largely by countries in Northern and Southern Africa" - Dr @MoetiTshidi @WHOAFRO


"The #COVID19 third wave in #Africa has taken a downwards slide, with a 23% decrease in new cases last week, driven largely by countries in Northern and Southern Africa. That’s the steepest drop in eight weeks since the peak in July." - Dr @MoetiTshidi

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Promisingly, all provinces across South Africa have passed their peaks and now showing a sustained decline in #COVID19 cases and test positivity rates @rid1tweets
Africa




19-JUL-2021 :: So, my Point is this, our Attention span is short and Many Folks seem to feel we are in the final Act of the COVID-19 Play. I would be limit short that particular narrative.



Drinking the Kool-Aid 
https://bit.ly/3hCJjXG

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Many media outlets and pharmaceutical executives claim that Africa has not been badly hit by Covid-19. The evidence shows the opposite is true. @thecontinent_ Laura López González
Africa



The world has used a lack of data to tell itself that Africa has emerged from the Covid-19 pandemic relatively unscathed. 

It is a dangerous and deeply rooted fiction – and a tacit justification for one of this century’s darkest moments

a recent Time magazine headline read, “Why Africa’s Covid-19 outbreak hasn’t been as bad as everyone feared.”

In Africa, there’s absolutely no data to say the continent has been spared. In fact, Professor Tom Moultrie, a demographer from the University of Cape Town, thinks the notion should be retired altogether.
“The reason why we think there’s no Covid in much of Africa is simply because we don’t know where to find those deaths... that doesn’t at all mean to say that they are not happening,” Moultrie told The Continent.

Moultrie tracks uncounted Covid-19 deaths in South Africa. “I buy the argument that we have a younger population, but that is not enough. Without hard evidence built off reliable data from health and vital registration systems and reasonably large sample sizes of testing and mortality tracking, we simply cannot say that Africa has been spared.”

We also may never know Covid-19’s true body count in Africa for two reasons: A lack of testing and a dearth of records.



''viruses exhibit non-linear and exponential characteristics''



28-MAR-2021  we are seeing a sustained acceleration in mutant viruses.




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A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa @ScienceMagazine
Africa


The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. 

Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories.

As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1 and C.1.1.

. Throughout the pandemic, it has been noted that Africa accounts for a relatively low proportion of reported cases and deaths – by the end of April 2021, there had been ~4.5 million cases and ~120000 deaths on the continent, corresponding to less than 4% of the global burden. 

However, emerging data from seroprevalence surveys and autopsy studies in some African countries suggests that the true number of infections and deaths may be several fold higher than reported 

The first cases of COVID-19 on the African continent were reported in Nigeria, Egypt and South Africa between mid-February and early March 2020, and most countries had reported cases by the end of March 2020 (6–8). 

These early cases were concentrated amongst airline travellers returning from regions of the world with high levels of community transmission. 

Intensified sampling by NGS-SA in the Eastern Cape Province of South Africa in November 2020, in response to a rapid resurgence of cases, led to the detection of B.1.351 (501Y.V2) 

Here, we perform phylogenetic and phylogeographic analysis of SARS-CoV-2 genomic data from 33 African countries and two overseas territories to help characterize the dynamics of the pandemic in Africa. 

We show that the early introductions were predominantly from Europe, but that as the pandemic progressed there was increasing spread between African countries. 

We also describe the emergence and spread of a number of key SARS-CoV-2 variants in Africa, and highlight how the spread of B.1.351 (501Y.V2) and other variants contributed to the more severe second wave of the pandemic in many countries.

By 5 May 2021, 14504 SARS-CoV-2 genomes had been submitted to the GISAID database (18) from 38 African countries and two overseas territories (Mayotte and Réunion) 

SARS-CoV-2 genomic data
By 5 May 2021, 14504 SARS-CoV-2 genomes had been submitted to the GISAID database (18) from 38 African countries and two overseas territories (Mayotte and Réunion) (Fig. 1A). 

Overall, this corresponds to approximately one sequence per ~300 reported cases. 

Almost half of the sequences were from South Africa (n=5362), consistent with it being responsible for almost half of the reported cases in Africa. 

Overall, the number of sequences correlates closely with the number of reported cases per country (Fig. 1B). 

The countries/territories with the highest coverage of sequencing (defined as genomes per reported case) are Kenya (n=856, one sequence per ~203 cases), Mayotte (n=721, one sequence per ~21 cases), and Nigeria (n=660, one sequence per ~250 cases). 

Although genomic surveillance started early in many countries, few have evidence of consistent sampling across the whole year. 

Half of all African genomes were deposited in the first ten weeks of 2021, suggesting intensified surveillance in the second wave following the detection of B.1.351/501Y.V2 and other variants (Fig. 1, C and D).

Genetic diversity and lineage dynamics in Africa
Of the 10326 genomes retrieved from GISAID by the end of March 2021, 8,746 genomes passed quality control (QC) and met the minimum metadata requirements. 

These genomes from Africa were compared in a phylogenetic framework with 11891 representative genomes from around the world. 

Ancestral location state reconstruction of the dated phylogeny (hereafter referred to as discrete phylogeographic reconstruction) allowed us to infer the number of viral imports and exports between Africa and the rest of the world, and between individual African countries. 

African genomes in this study spanned the whole global genetic diversity of SARS-CoV-2, a pattern that largely reflects multiple introductions over time from the rest of the world (Fig. 2A).

In total, we detected at least 757 (95% CI: 728 - 786) viral introductions into African countries between the start of 2020 and February 2021, over half of which occurred before the end of May 2020. 

While the early phase of the pandemic was dominated by importations from outside Africa, predominantly from Europe, there was then a shift in the dynamics, with an increasing number of importations from other African countries as the pandemic progressed (Fig. 2, B and C). 

A rarefaction analysis in which we systematically subsampled genomes shows that vastly more introductions would have likely been identified with increased sampling in Africa or globally, suggesting that the introductions we identified are really just the “ears of the hippo,” or tip of the iceberg (fig. S1).
South Africa, Kenya and Nigeria appear as major sources of importations into other African countries (Fig. 2D), although this is likely to be influenced by these three countries having the greatest number of deposited sequences. 

Particularly striking is the southern African region, where South Africa is the source for a large proportion (~80%) of the importations to other countries in the region. 

The North African region demonstrates a different pattern to the rest of the continent, with more viral introductions from Europe and Asia (particularly the Middle East) than from other African countries (fig. S2).
Africa has also contributed to the international spread of the virus with at least 324 (95% CI: 728 - 786) exportation events from Africa to the rest of the world detected in this dataset. 

Consistent with the source of importations, most exports were to Europe (41%), Asia (26%) and North America (14%). 

As with the number of importations exports were relatively evenly distributed over the one year period (fig. S3). 

However, an increase in the number of exportation events occurred between December 2020 and March 2021, which coincided with the second wave of infections in Africa and with some relaxations of travel restrictions around the world.
The early phase of the pandemic was characterized by the predominance of lineage B.1. 

This was introduced multiple times to African countries and has been detected in all but one of the countries included in this analysis. 

After its emergence in South Africa, B.1.351 became the most frequently detected SARS-CoV-2 lineage found in Africa (n=1,769, ~20%) (Fig. 1C). 

It was first sampled on 8 October 2020 in South Africa (13) and has since spread to 20 other African countries.
As air travel came to an almost complete halt in March/April 2020, the number(s) of detectable viral imports into Africa decreased and the pandemic entered a phase that was characterized in sub-Saharan Africa by sustained low levels of within-country movements and occasional international viral movements between neighboring countries, presumably via road and rail links between these. 

Though some border posts between countries were closed during the initial lockdown period (table S1), others remained open to allow trade to continue. 

Regional trade in southern Africa was only slightly impacted by lockdown restrictions and quickly rebounded to pre-pandemic levels (fig. S4) following the relaxation of restrictions between June 2020 and December 2020.
Although lineage A viruses were imported into several African countries, they only account for 1.3% of genomes sampled in Africa. 

Despite lineage A viruses initially causing many localized clustered outbreaks, each the result of independent introductions to several countries (e.g., Burkina Faso, Cote d’Ivoire and Nigeria), they were later largely replaced by lineage B viruses as the pandemic evolved. 

This is possibly due to the increased transmissibility of B lineage viruses by virtue of the D614G mutation in spike (19, 20). 

However, there is evidence of an increasing prevalence of lineage A viruses in some African countries (11). In particular, A.23.1 emerged in East Africa and appears to be increasing rapidly in prevalence in Uganda and Rwanda (11). 

Furthermore, a highly divergent variant from lineage A was recently identified in Angola from individuals arriving from Tanzania (21).
Emergence and spread of new SARS-CoV-2 variants
In order to determine how some of the key SARS-CoV-2 variants are spreading within Africa, we performed phylogeographic analyses on the VOC B.1.351, the variant of interest (VOI) B.1.525, and on two additional variants that emerged and that we designated as VOIs for this analysis (A.23.1 and C.1.1). 

These African VOCs and VOIs have multiple mutations on Spike glycoprotein and molecular clock analysis of these four datasets provided strong evidence that these four lineages are evolving in a clocklike manner (Fig. 3, A and B).

B.1.351 was first sampled in South Africa in October 2020, but phylogeographic analysis suggests that it emerged earlier, around August 2020. 

It is defined by ten mutations in the spike protein, including K417N, E484K and N501Y in the receptor-binding domain (Fig. 3B). 

Following its emergence in the Eastern Cape, it spread extensively within South Africa (Fig. 4A). 

By November 2020, the variant had spread into neighboring Botswana and Mozambique and by December 2020 it had reached Zambia and Mayotte. 

Within the first three months of 2021, further exports from South Africa into Botswana, Zimbabwe, Mozambique and Zambia occurred. 

By March 2021, B.1.351 had become the dominant lineage within most Southern African countries as well as the overseas territories of Mayotte and Réunion (fig. S5). 

Our phylogeographic reconstruction also demonstrates movement of B.1.351 into East and Central Africa directly from southern Africa. 

Our discrete phylogeographic analysis of a wider sample of B.1.351 isolates demonstrate the spread of the lineage into West Africa. 

This patient from West Africa had a known travel history to Europe so it possible the patient acquired the infection while in Europe or in transit and not from other African sources (fig. S6).

B.1.525 is a VOI defined by six substitutions in the spike protein (Q52R, A67V, E484K, D614G, O677H and F888L), and two deletions in the N-terminal domain (HV69-70Δ and Y144Δ). 

This was first sampled in the United Kingdom in mid-December 2020, but our phylogeographic reconstruction suggests that the variant originated in Nigeria in November 2020 [95% highest posterior density (HPD) 2020-11-01 to 2020-12-03] (Fig. 4B). 

Since then it has spread throughout much of Nigeria and neighboring Ghana. 

Given sparse sampling from other neighboring countries within West and Central Africa (Fig. 1, A and C), the extent of the spread of this VOI in the region is not clear. Beyond Africa, this VOI has spread to Europe and the US (fig. S6).
We designated A.23.1 and C.1.1 as VOIs for the purposes of this analysis, as they present good examples of the continued evolution of the virus within Africa (11, 13). 

Lineage A.23, characterized by three spike mutations (F157L, V367F and Q613H), was first detected in a Ugandan prison in Amuru in July 2020 (95% HPD: 2020-07-15 to 2020-08-02). 

From there, the lineage was transmitted to Kitgum prison, possibly facilitated by the transfer of prisoners. 

Subsequently, the A.23 lineage spilled into the general population and spread to Kampala, adding other spike mutations (R102I, L141F, E484K, P681R) along with additional mutations in nsp3, nsp6, ORF8 and ORF9, prompting a new lineage classification, A.23.1 (Fig. 3, A and B). 

Since the emergence of A.23.1 in September 2020 (95% HPD: 2020-09-02 to 2020-09-28), it has spread regionally into neighboring Rwanda and Kenya and has now also reached South Africa and Botswana in the south and Ghana in the west (Fig. 4C). 

However, our phylogeographic reconstruction of A.23.1 suggests that the introduction into Ghana may have occurred via Europe (fig. S6), whereas the introductions into southern Africa likely occurred directly from East Africa. 

This is consistent with epidemiological data suggesting that the case detected in South Africa was a contact of an individual who had recently travelled to Kenya.
Lineage C.1 emerged in South Africa in March 2020 (95% HPD: 2020-03-13 to 2020-04-17) during a cluster outbreak prior to the first wave of the epidemic (13).

 C.1.1 is defined by the spike mutations S477N, A688S, M1237I and also contains the Q52R and A67V mutations similar to B.1.525 (Fig. 3B). 

A continuous trait phylogeographic reconstruction of the movement dynamics of these lineages suggests that C.1 emerged in the city of Johannesburg and spread within South Africa during the first wave (Fig. 4D). 

Independent exports of C.1 from South Africa led to regional spread to Zambia (June-July, 2020) and Mozambique (July-August 2020), and the evolution to C.1.1 seems to have occurred in Mozambique around mid-September 2020 (95% HPD: 2020-09-07 to 2020-10-05). 

In depth analysis of SARS-CoV-2 genotypes from Mozambique suggest that the C.1.1. lineage was the most prevalent in the country until the introduction of B.1.351, which has dominated the epidemic since (fig. S5).
The VOC B.1.1.7, which was first sampled in Kent, England in September 2020 (22), has also increased in prevalence in several African countries (fig. S5) 

To date, this VOC has been detected in eleven African countries, as well as the Indian Ocean islands of Mauritius and Mayotte (fig. S7). 

The time-resolved phylogeny suggests that this lineage was introduced into Africa on at least 16 occasions between November 2020 and February 2021 with evidence of local transmission in Nigeria and Ghana.

Conclusions
Our phylogeographic reconstruction of past viral dissemination patterns suggests a strong epidemiological linkage between Europe and Africa, with 64% of detectable viral imports into Africa originating in Europe and 41% of detectable viral exports from Africa landing in Europe (Fig. 1C). 

This phylogeographic analysis also suggests a changing pattern of viral diffusion into and within Africa over the course of 2020. 

In almost all instances the earliest introductions of SARS-CoV-2 into individual African countries were from countries outside Africa.
High rates of COVID-19 testing and consistent genomic surveillance in the south of the continent have led to the early identification of VOCs such as B.1.351 and VOIs such as C.1.1 (13). 

Since the discovery of these southern African variants, several other SARS-CoV-2 VOIs have emerged in different parts of the world, including elsewhere on the African continent, such as B.1.525 in West Africa and A.23.1 in East Africa. 

There is strong evidence that both of these VOIs are rising in frequency in the regions where they have been detected, which suggests that they may possess higher fitness than other variants in these regions. 

Although more focused research on the biological properties of these VOIs is needed to confirm whether they should be considered VOCs, it would be prudent to assume the worst and focus on limiting their spread. 

It will be important to investigate how these different variants compete against one another if they occupy the same region.
Our focused phylogenetic analysis of the B.1.351 lineage revealed that in the final months of 2020 this variant spread from South Africa into neighboring countries, reaching as far north as the DRC by February 2021. 

This spread may have been facilitated through rail and road networks that form major transport arteries linking South Africa’s ocean ports to commercial and industrial centres in Botswana, Zimbabwe, Zambia and the southern parts of the DRC. 

The rapid, apparently unimpeded spread of B.1.351 into these countries suggests that current land-border controls that are intended to curb the international spread of the virus are ineffective. 

Perhaps targeted testing of cross-border travellers, genotyping of positive cases and the focused tracking of frequent cross-border travellers such as long distance truckers, would more effectively contain the spread of future VOCs and VOIs that emerge within this region.
The dominance of VOIs and VOCs in Africa has important implications for vaccine rollouts on the continent. 

For one, slow rollout of vaccines in most African countries creates an environment in which the virus can replicate and evolve: this will almost certainly produce additional VOCs, any of which could derail the global fight against COVID-19. 

On the other hand, with the already widespread presence of known variants, difficult decisions balancing reduced efficacy and availability of vaccines have to be made. 

This also highlights how crucial it is that trials are done. From a public health perspective, genomic surveillance is only one item in the toolkit of pandemic preparedness. 

It is important that such work is closely followed by genotype to phenotype research to determine the actual significance of continued evolution of SARS-CoV-2 and other emerging pathogens.
The rollout of vaccines across Africa has been painfully slow (figs. S8 and S9). 

There have, however, been notable successes that suggest the situation is not hopeless. 

The small island nation of the Seychelles had vaccinated 70% of its population by May 2021. 

Morocco has kept pace with many developed nations and by mid-March had vaccinated ~16% of its population. 

Rwanda, one of Africa’s most resource constrained countries, had, within three weeks of obtaining its first vaccine doses in early March, managed to provide first doses to ~2.5% of its population. 

For all other African countries, at the time of writing, vaccine coverage (first dose) was <1.0% of the general population.
The effectiveness of molecular surveillance as a tool for monitoring pandemics is largely dependent on continuous and consistent sampling through time, rapid virus genome sequencing and rapid reporting. 

When this is achieved, molecular surveillance can ensure the early detection of changing pandemic characteristics. 

Further, when such changes are discovered, molecular surveillance data can also guide public health responses. 

In this regard, the molecular surveillance data that are being gathered by most African countries are less useful than they could be. 

For example, the time-lag between when virus samples are taken and when sequences for these samples are deposited in sequence repositories is so great in some cases that the primary utility of genomic surveillance data is lost (fig. S10). 

This lag is driven by several factors depending on the laboratory or country in question: 

(i) lack of reagents due to disruptions in global supply chains, 

(ii) lack of equipment and infrastructure within the originating country, 

(iii) scarcity of technical skills in laboratory methods or bioinformatic support, and 

(iv) hesitancy by some health officials to release data. More recent sampling and prompt reporting is crucial to reveal the genetic characteristics of currently circulating viruses in these countries.
The patchiness of African genomic surveillance data is therefore the main weakness of our study. 

However, there is evidence that the situation is improving, with ~50% of African SARS-CoV-2 genome sequences having been submitted to the GISAID database within the first 10-weeks of 2021. 

While the precise factors underlying this surge in sequencing effort are unclear, important drivers are almost certainly both increased global interest in genomic surveillance following the discovery of multiple VOCs and VOIs since December 2020. 

We cannot reject that the observed increase in exports from Africa may be due to intensified sequencing activity following the detection of variants around the world. 

It is important to note here that phylogeographic reconstruction of viral spread is highly dependent on sampling where there is the caveat that the exact routes of viral movements between countries cannot be inferred if there is no sampling in connecting countries. 

Furthermore, our efforts to reconstruct the movement dynamics of SARS-CoV-2 across the continent are almost certainly biased by uneven sampling between different African countries. 

It is not a coincidence that we identified South Africa, Kenya and Nigeria, which have sampled and sequenced the most SARS-CoV-2 genomes, as major sources of viral transmissions between sub-Saharan African countries. 

However, these countries had also the highest number of infections, which may decrease the sampling biases (Fig. 1A).
The reliability of genomic surveillance as a tool to prevent the emergence and spread of dangerous variants is dependent on the intensity with which it is embraced by national public health programs. 

As with most other parts of the world, the success of genomic surveillance in Africa requires more samples being tested for COVID-19, higher proportions of positive samples being sequenced within days of sampling, and persistent analyses of these sequences for concerning signals such as 

(i) the presence of novel non-synonymous mutations at genomic sites associated with pathogenicity and immunogenicity, 

(ii) evidence of positive selection at codon sites where non-synonymous mutations are observed, and 

(iii) evidence of lineage expansions. 

In spite of limited sampling, Africa has identified many of the VOCs and VOIs that are being transmitted across the world. 

Detailed characterization of the variants and their impact on vaccine induced immunity is of extreme importance. 

If the pandemic is not controlled in Africa, we may see the production of vaccine escape variants that may profoundly affect the population in Africa and across the world.

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Fig. 1 SARS-CoV-2 sequences in Africa.
Africa



(A) Map of the African continent with the number of SARS-CoV-2 sequences reflected in GISAID as of 5 May 2021. 

(B) Regression plot of the number of viral sequences vs. the number of reported COVID-19 cases in various African countries as of 5 May 2021. Countries with >500 sequences are labeled. 

(C) Progressive distribution of the top 20 PANGO lineages on the African continent. 

(D) Temporal sampling of SARS-CoV-2 sequences in African countries (ordered by total number of sequences) through time with VOCs of note highlighted and annotated according to their PANGO lineage assignment.

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Fig. 2 Phylogenetic reconstruction of the SARS-CoV-2 pandemic on the Africa continent.
Africa



(A) Time resolved Maximum Likelihood tree containing 8,746 high quality African SARS-CoV-2 near-full-genome sequences analyzed against a backdrop of global reference sequences. Variants of interest (VOI) and concern (VOC) are highlighted on the phylogeny. 

(B) Sources of viral introductions into African countries characterized as external introductions from the rest of the world vs internal introductions from other African countries. 

(C) Total external viral introductions over time into Africa. 

(D) The number of viral imports and exports into and out of various African countries depicted as internal (between African countries in pink) or external (between African and non-African countries in blue and grey).

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Fig. 3 Genetic profile of VOCs and VOIs under investigation.
Africa



(A) Root-to-tip regression plots for four lineages of interest. C.1 and A.23 show continued evolution into VOIs C.1.1 and A.23.1 respectively. 

(B) Genome maps of four VOCs/VOIs where the spike region is shown in detail and in color and the rest of the genome is shown in grey. ORF: open reading frame, NTD: N-terminal domain, RBD: receptor binding domain, RBM: receptor binding motif, SD1: subdomain 1 and SD2: subdomain 2.

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Fig. 4 Phylogeographic reconstruction of the spread of four VOCs/VOIs across the African continent using sequences showing strict continuous transmission across geographical regions.
Africa


(A to D) Curved lines denote the direction of transmission in the anti-clockwise direction. Solid lines show transmission paths as inferred by phylogeographic reconstruction and colored by date, whereas dashed lines show known travel history of the particular case considered.

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West Africa’s latest coup is bringing back memories of the 1980s. Bloomberg Next Africa
Africa



There have been four military takeovers in the region this year, including two in Mali, a level of upheaval reminiscent of more than 30 years ago. 

While the overthrows have been condemned by regional blocs and foreign powers, little has been done to reverse them. 

France even backed the April takeover of Chad by the son of slain leader Idriss Deby in the interest of stability.
The leaders of Mali and Guinea can be said to have brought their downfalls on themselves. 

They both frustrated youthful populations with economic mismanagement, corruption and overbearing security forces.
They have also been reluctant to relinquish power. Alpha Conde, Guinea’s deposed leader, forced through an unpopular constitutional amendment to serve a third term despite being 83 years old.
In the 1970s and 1980s, “the armed forces overthrew aging and corrupt powers,” according to Vincent Foucher and Rinaldo Depagne of International Crisis Group. 

The ousted leaders of today have similarly won little regional backing, given their “practices and way of governing are very undemocratic and difficult to support,” they said.
Elsewhere in the region, Alassane Ouattara of Ivory Coast and Faure Gnassingbe of Togo have been in power for 11 and 16 years respectively. Paul Biya of Cameroon, who is 88, has led his country since 1982. Patrice Talon of Benin retained power in a questionable election.

They must be looking over their shoulders.


Turning to Africa




We are getting closer and closer to the Virilian Tipping Point

Political leadership in most cases completely gerontocratic will use violence to cling onto Power but any Early Warning System would be warning a Tsunami is coming



Re-election, Death and Putsch: A zero Sum Game. @hervegogo





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GUINEA Sidelined legionnaire grabs the reins @Africa_Conf
Africa


Fights over military organisation and President Condé's tumbling legitimacy set the stage for Colonel Doumbouya's putsch
A decade after being sworn into office by judges in vermilion and ermine, President Alpha Condé of Guinea became the prisoner of an elite military unit that stormed the presidential palace in the small hours of 5 September. 

A remarkable image framed his fall: soldiers armed with assault rifles posing in front of a Condé in half-unbuttoned shirt and vest, immediately after his capture. 

As he was driven to an unknown destination, jammed between two soldiers, crowds celebrated in the streets of the capital, Conakry, shouting 'Liberté! Liberté!'
Hailed as a new democratic hope for Guinea, ending 50 years of civil and military dictatorship, Condé promised from the outset of his presidency to fight corruption, winning international plaudits. 

Now, the African Union (AU) and the Economic Community of West African States (Ecowas) – which was meeting as Africa Confidential went to press – have to decide how to react (AC Dispatches 7/9/21, Regional summit due to meet Thursday on post-coup crisis). 

They, along with France, the UN and the EU, have condemned the coup and called for Conde's release, but none of these bodies have called for his reinstatement. 

The regional blocks are increasingly on the back foot as coups become more frequent in West and Central Africa. 

In Guinea, Ecowas and the AU have lost much credibility by their failure to condemn Condé's changing the constitution ahead of presidential elections last year, allowing him to stay in power for a third term.
While Condé's manipulation of the electoral rules and brutal crackdowns on opposition demonstrations laid the ground for Sunday's coup, these were not the only factors behind his sudden fall at the hands of Colonel Mamady Doumbouya's 300-strong special forces unit.
The background to the putsch is rivalry between elite military units and a tussle for influence among senior figures in Condé's Malinké community that local elders in Kankan, the capital of the north-eastern Haute Guinée region, were unable to resolve.
Defence Minister Mohamed Diané, considered to be Condé's preferred heir, was steadily marginalising Doumbouya's 300-strong Groupement des Forces Spéciales (GPS) – a unit the future putschist had been hand-picked by Condé to create in 2018. 

Fears over the GPS's loyalties led Diané to arrange its transfer out of downtown Conakry to a south-western provincial base, close to the Sierra Leone border.
A former soldier in the French foreign legion, Doumbouya only returned home in 2011, meaning his career was untainted by any connection to the brutalities associated with the final years of authoritarian and military rule. 

These included a 2009 massacre of over 100 opposition supporters at a rally protesting against former military ruler Moussa Dadis Camara's plan to stand in 2010 presidential elections, abuses for which Camara and others have been indicted but still not tried.
Pursuing a career back in the Guinean army, he was sent for staff officer training at the École de Guerre in France and then picked by Condé to establish the new GPS to provide an elite unit trained to deal with the terrorist threats that have become a growing concern for governments across West Africa. 

It was therefore based in central Conakry, in part of the Palais du Peuple congress centre.
But when Doumbouya bluntly told a French military conference about the struggles he faced in trying to secure government resources for his new force, word got back to an infuriated Diané. Relations between the two men steadily deteriorated.
The Defence Minister brushed aside efforts by Kankan community elders to mediate between the two men, both of whom are Malinké. 

He opted instead to marginalise Doumbouya by creating a rival unit, the Bataillon d'Intervention Rapide (BIR) – for which the establishment decree, seen by Africa Confidential, was issued on 1 June this year.
The decree, signed by Condé, says the BIR was set up to 'intervene quickly to back up other border units in the fight against all kinds of threats'. 

It says the BIR is 'the main means of dissuasion, reaction and coercion of the Army. Robust, supple, reactive, it constitutes a genuine rapid reaction force.'
The enforced transfer of the GPS base was further intended to demotivate the unit, with its soldiers stuck in sleepy Forecariah, away from the temptations of Conakry, even though this distanced them from the capital city installations they had been created to protect.
But there are indications in Conakry that the roots of the coup may stretch back earlier than these ructions and that significant elements of the military had been mulling a putsch for some time.
The depth of popular resentment against Condé had been evident for many months, and it gradually spread beyond the normal sources of support for the opposition to substantial sections of the Malinké population and even some members of the ruling Rassemblement du Peuple Guinéen (RPG). 

It was also widely known that many West African leaders had been exasperated by Condé's determination to prolong his stay in power, even at the risk of fuelling instability.
But senior military, including the gendarmerie, had another concern. 

As Condé's repressive stance hardened, the security forces increasingly found themselves called upon to crush protest and, with the long history of confrontation on Conakry's streets, such situations all too often have seen troops resort to live rounds.
As the deaths piled up, military commanders became concerned about the risk of pursuit by international human rights campaigns and, potentially, institutions such as the International Criminal Court.
When the moment came to act, Doumbouya had the endorsement of other senior figures – in his immediate post-coup appearance he was flanked by Colonel Balla Samoura, regional director of the gendarmerie in Conakry, and the gendarmerie chief of staff, General Ibrahima Baldé.
But ethnic sensitivities still weigh heavily. Officers from the Peuhl (or Fulani) – Guinea's largest ethnic group at 40% of the population, and largely supportive of the opposition – judged it wisest to leave their Malinké colleagues to take the front roles, to avoid any risk of the putsch being perceived as motivated by ethnic factors.
The soldiers now at the helm in Guinea have manoeuvred to establish themselves in a position of strength before the inevitable hard bargaining with Ecowas begins. 

Doumbouya's first appearance before the cameras – in standard putschist military fatigues and sunglasses – delivered stentorian condemnation of the abuse of power and human rights under the ousted head of state, to justify the army's intervention.
Constitutional rights campaigners celebrated the release of dozens of political detainees on Tuesday, and the coup secured the public endorsement of perennial presidential challenger Cellou Dalein Diallo, leader of the Alliance Nationale pour l'Alternance et la Démocratie and an ethnic Peuhl, who commands widespread support in the Fouta Djalon region of western Guinea.
Senior figures in Condé's RPG seem to be divided. But the party's activists have quickly adjusted to the new political environment, sticking up posters in support of Doumbouya's Comité national du rassemblement et du développement junta.
The real challenge for Ecowas, backed up by the AU and the wider international community, will be to secure the putschists' commitment to a clear, time-tabled transition back to constitutional democratic structures and to ensure they stick to that. 

Reports have suggested Doumbouya may have got to know Assimi Goïta, the 2020 Mali putschist now suspected of hoping to prolong his transitional rule until 2023, while both were on a United States-organised Flintlock regional training exercise.
Guinea's new military masters briefly shut external borders on 5 September, but reopened them for trade the next day, inviting mining companies to resume normal operations and ordering civil servants back to work.
Members of the old government and other senior constitutional figures were summoned to a meeting with Doumbouya in a marquee outside Conakry's congress centre on 6 September and then sent home after being told to surrender their travel documents. 

At this same meeting,  Doumbouya declared his intention to form a national unity government to run the transition. 

The supportive comments from Diallo and the Front National pour la Défense de la Constitution rights campaign suggest that he may well manage to draw senior figures from across the political spectrum and civil society into such a united front.
The warm welcome for Condé's overthrow among so many in Guinea is no surprise.
A veteran opposition campaigner who had served jail time for challenging the authoritarian President Lansana Conté in the 1998 election, he finally secured office in the country's first democratic election 12 years later. 

Condé gradually consolidated civilian institutions during his first years in power, but proved deeply wary of sharing authority, postponing legislative elections until EU financial pressure forced him to organise polls in 2013.
Once re-elected for a second term, he increasingly focused on preparing the ground for a constitutional referendum in March 2020, to scrap term limits so he could stand for a third stint in office (AC Vol 61 No 22, Condé shrugs off poll doubts). 

The referendum, a heavily manipulated affair, cleared the way for his predictable victory in October's tightly managed presidential contest, boycotted by many opponents.
Human rights deteriorated steadily during Condé's second term, with regular intimidation of opponents, a growing number of political detentions and often lethal clashes between the security forces and youthful protesters. 

Last year proved particularly brutal, with scores of protesters shot by the security forces, while numerous civil society and opposition figures, particularly Diallo's supporters, were jailed.

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Alpha Condé the man known as “Le Professeur” @mailandguardian @thecontinent_
Africa





Despite some minor improvements, basic services such as access to electricity and running water remain a luxury in Guinea. 

The country’s roads are in terrible shape, perhaps the worst in West Africa. 

And despite being the world’s second- largest producer of Bauxite, this vast mineral wealth has seemed to benefit only a handful of individuals in Condé’s orbit.
But it was in seeking to change the constitution, to allow himself to run for a third term in office, that the president’s despotic nature became impossible to ignore.

His frequent insults against his own people – “Guineans are afraid, they are like a turtle, you have to put a fire in their behinds,” he said at a conference in February – made him even less popular.
“The Guinean political system lives by recycling its authoritarian spirit,” said Amadou Sadjo Barry, a professor of philosophy. “Alpha Condé has helped renew the logic of arbitrariness and establish military legitimacy.”

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How the mighty have fallen When your fall from grace is captured on camera @mailandguardian @thecontinent_ @simonallison
Africa



It is not, by any normal measure, a particularly good photograph. The lighting is all wrong. The resolution is poor. The framing is not balanced. 

And yet, of the thousands upon thousands of photographs that exist of Alpha Condé, this is the one by which he will be forever defined.
It shows the Guinean president – the former president – in the immediate aftermath after the military coup which deposed him on Sunday. 

Surrounded by heavily armed soldiers, Condé is slouched on a couch. His shirt is buttoned up all wrong and he is clearly seething. 

The photo is so compelling because it captures the very moment when Condé realises that everything he has ever worked for has been taken away from him; that the power which he has fought so hard to keep is no longer his.
He has fallen from grace, and this extraordinarily intimate image – stripped of all the pomp and ceremony and grandeur of your typical presidential photograph – is proof of just how far he has fallen.
Condé is not the first president, and he will not be the last, to have his humiliation captured on camera for the world to see. 

The images are often grainy – mutinous soldiers make for poor photographers, or perhaps they are stills taken from video footage – but what they lack in clarity they make up for in emotional heft.
Other classics in this genre include:

Robert Mugabe, on the sofa next to his wife Grace, surrounded by the “friends” who have been sent to persuade him to step down. On the coffee table in front of them – alongside the box of tissues provided to mop up their tears – is a folder containing the resignation letter Mugabe will sign just seconds after this picture is taken.
Muammar Gaddafi, face battered and bloodied, in the minutes before his death at the hands of the opposition fighters who found him cowering in a drain pipe. 

Yahya Jammeh, clutching on to the last remnants of his status and dignity as he boards the private plane that will ferry him into unhappy exile.
Hosni Mubarak, in a cage in a Cairo courtroom, being made to answer for his crimes.
Jacob Zuma, shock and fury written all over his face, as Cyril Ramaphosa is announced as the next leader of the ANC 

Laurent Gbagbo being arrested, at home in his vest, after failing to convince anyone except his own diehard supporters that he won the 2010 Ivorian election.
There is something utterly fascinating about seeing these once all-powerful presidents in positions of powerlessness; the schadenfreude, yes, but also the reminder that nothing on this earth is permanent or immovable. 

It is a lesson that other long-term occupants of presidential palaces might be wise to heed, before they get their own entry into this particular hall of shame.

Sic transit gloria mundi is a Latin phrase that means "Thus passes the glory of the world." It has been interpreted as "Worldly things are fleeting''


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.@WilhelmSasnal Gaddafi 2 2011 @Tate
Africa




“In too many places, in too many ways, the region’s foundations are sinking into the sand,” said Secretary Hillary Clinton. 
@csmonitor




“Those who cling to the status quo may be able to hold back the full impact of their countries’ problems for a little while, but not forever, If leaders don’t offer a positive vision and give young people meaningful ways to contribute, others will fill the vacuum.”




John Donne wrote:
"...Therefore, send not to know
For whom the bell tolls,
It tolls for thee..."

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A trip to Kigali by France’s President Emmanuel Macron, who said Rwanda is “at the heart of [the] capacity that France may have to help bring out regional responses” to crises such as that in Cabo Delgado. @thecontinent_
Africa


If security conditions continue to improve in Cabo Delgado, the TotalEnergies project could restart operations in 12-18 months, according to African Development Bank president Akinwumi Adesina

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Allied Front | Gambian President Adama Barrow and former dictator Yahya Jammeh are joining forces ahead of December elections in a pact that will test the incumbent’s commitment to seek justice for alleged victims of his predecessor. @bpolitics
Africa


Jammeh, who ruled the West African nation for 22 years, was forced to resign after losing a 2016 vote to Barrow. The $1-billion economy, which depends on tourism for nearly a third of its GDP, has never seen a smooth transfer of power. 

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War between Tigray's forces and Federal forces, backed by Eritrea, is set to drag on for several more months. Both sides claim they are inflicting ever heavier military losses on the other after an upsurge of fighting in recent weeks. @Africa_Conf
Africa


February 1st 2021 ‘The genie out of the bottle’ @AfricanBizMag





It’s impossible for the state to manage a guerrilla war up there and at the same time manage to control the rest of the country.


As a reminder, this was the scene in Mekele last New Year's Eve, as we awaited results of the disputed regional elections: @rcoreyb






'War makes for bitter men. Heartless and savage men,” Abiy said in his Nobel prize lecture. @FT @davidpilling 



The falcon cannot hear the falconer;


Turning and turning in the widening gyre
The falcon cannot hear the falconer;
Things fall apart; the centre cannot hold;
Mere anarchy is loosed upon the world,
The blood-dimmed tide is loosed, and everywhere The ceremony of innocence is drowned;
The best lack all conviction, while the worst Are full of passionate intensity.








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by Aly Khan Satchu (www.rich.co.ke)
 
 
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September 2021
 
 
 
 
 
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